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Yorodumi- PDB-1mcb: PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mcb | ||||||
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Title | PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS | ||||||
Components |
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Keywords | IMMUNOGLOBULIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å | ||||||
Authors | Edmundson, A.B. / Harris, D.L. / Fan, Z.-C. / Guddat, L.W. | ||||||
Citation | Journal: Proteins / Year: 1993 Title: Principles and pitfalls in designing site-directed peptide ligands. Authors: Edmundson, A.B. / Harris, D.L. / Fan, Z.C. / Guddat, L.W. / Schley, B.T. / Hanson, B.L. / Tribbick, G. / Geysen, H.M. #1: Journal: Mol.Immunol. / Year: 1987 Title: The Binding of Opioid Peptides to the Mcg Light Chain Dimer: Flexible Keys and Adjustable Locks Authors: Edmundson, A.B. / Ely, K.R. / Herron, J.N. / Cheson, B.D. #2: Journal: Mol.Immunol. / Year: 1985 Title: Binding of N-Formylated Chemotactic Peptides in Crystals of the Mcg Light Chain Dimer: Similarities with Neutrophil Receptors Authors: Edmundson, A.B. / Ely, K.R. #3: Journal: Mol.Immunol. / Year: 1984 Title: A Search for Site-Filling Ligands in the Mcg Bence-Jones Dimer: Crystal Binding Studies of Fluorescent Compounds Authors: Edmundson, A.B. / Ely, K.R. / Herron, J.N. / Cheson, B.D. #4: Journal: Biochemistry / Year: 1974 Title: Binding of 2,4-Dinitrophenyl Compounds and Other Small Molecules to a Crystalline Lambdal-Type Bence-Jones Dimer Authors: Edmundson, A.B. / Ely, K.R. / Girling, R.L. / Abola, E.E. / Schiffer, M. / Westholm, F.A. / Fausch, M.D. / Deutsch, H.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mcb.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mcb.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 1mcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mcb_validation.pdf.gz | 384.4 KB | Display | wwPDB validaton report |
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Full document | 1mcb_full_validation.pdf.gz | 406.7 KB | Display | |
Data in XML | 1mcb_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 1mcb_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/1mcb ftp://data.pdbj.org/pub/pdb/validation_reports/mc/1mcb | HTTPS FTP |
-Related structure data
Related structure data | 1mccC 1mcdC 1mceC 1mcfC 1mchC 1mciC 1mcjC 1mckC 1mclC 1mcnC 1mcqC 1mcrC 1mcsC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: PEPTIDE BOND BETWEEN GLN A 6 AND PRO A 7 DEVIATE SIGNIFICANTLY FROM TRANS CONFORMATION ( 137.36 DEGREES) 2: CIS PROLINE - PRO A 145 / 3: CIS PROLINE - PRO B 145 4: RESIDUES PHE P 2 AND PRO P 4 ARE D FORMS OF THE AMINO ACIDS PEPTIDE BOND BETWEEN HIS P 3 AND PRO P 4 DEVIATE SIGNIFICANTLY FROM TRANS CONFORMATION ( 248.52 DEGREES) |
-Components
#1: Antibody | Mass: 22819.080 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6PIK1 #2: Protein/peptide | | Mass: 554.617 Da / Num. of mol.: 1 / Source method: obtained synthetically Sequence details | THE LIGHT CHAIN WAS SEQUENCED BY FETT AND DEUTSCH (1974) BIOCHEMIST | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.46 % | ||||||||||||||||||||
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Crystal grow | Details: THIS COMPLEX WAS PREPARED BY COCRYSTALLIZATION WITH THE PEPTIDE. | ||||||||||||||||||||
Crystal grow | *PLUS pH: 6.2 / Method: batch method | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Wavelength: 1 Å |
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Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
-Processing
Software |
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Refinement | Resolution: 2.7→6 Å / σ(F): 1.5 /
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Refinement step | Cycle: LAST / Resolution: 2.7→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 6 Å / σ(F): 1.5 / Rfactor obs: 0.204 / Num. reflection obs: 11140 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |